Iron in PDB 6zy0: Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant

Protein crystallography data

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant, PDB code: 6zy0 was solved by D.Leys, T.Halliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 106.66 / 2.13
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 176.346, 169.569, 107.799, 90.00, 98.33, 90.00
R / Rfree (%) 18.6 / 22.2

Other elements in 6zy0:

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant also contains other interesting chemical elements:

Cobalt (Co) 3 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 3 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant (pdb code 6zy0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant, PDB code: 6zy0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 6zy0

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Iron binding site 1 out of 24 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:25.8
occ:1.00
FE1 A:SF4701 0.0 25.8 1.0
SG A:CYS518 2.2 23.4 1.0
S3 A:SF4701 2.3 27.6 1.0
S4 A:SF4701 2.3 28.6 1.0
S2 A:SF4701 2.3 20.4 1.0
FE3 A:SF4701 2.7 23.6 1.0
FE2 A:SF4701 2.7 23.8 1.0
FE4 A:SF4701 2.7 23.8 1.0
CB A:CYS518 3.4 24.4 1.0
S1 A:SF4701 3.9 24.4 1.0
CB A:ARG473 3.9 19.8 1.0
N A:CYS518 4.0 24.8 1.0
CA A:CYS518 4.3 22.5 1.0
CG1 A:ILE474 4.3 17.9 1.0
CD A:ARG473 4.3 21.6 1.0
CG A:ARG473 4.5 20.2 1.0
N A:ILE474 4.5 18.1 1.0
SG A:CYS512 4.7 22.6 1.0
CA A:ARG473 4.7 15.8 1.0
N A:ARG473 4.8 20.0 1.0
SG A:CYS515 4.8 21.4 1.0
SG A:CYS568 4.9 24.7 1.0
N A:LYS517 4.9 21.6 1.0
C A:ARG473 4.9 16.1 1.0
NE A:ARG473 5.0 23.0 1.0

Iron binding site 2 out of 24 in 6zy0

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Iron binding site 2 out of 24 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:23.8
occ:1.00
FE2 A:SF4701 0.0 23.8 1.0
S4 A:SF4701 2.3 28.6 1.0
S3 A:SF4701 2.3 27.6 1.0
SG A:CYS515 2.3 21.4 1.0
S1 A:SF4701 2.3 24.4 1.0
FE1 A:SF4701 2.7 25.8 1.0
FE3 A:SF4701 2.7 23.6 1.0
FE4 A:SF4701 2.7 23.8 1.0
CB A:CYS515 3.0 19.9 1.0
CD A:PRO569 3.8 23.2 1.0
S2 A:SF4701 3.9 20.4 1.0
CA A:CYS515 4.2 20.8 1.0
C A:CYS515 4.3 23.3 1.0
N A:LYS517 4.3 21.6 1.0
CG A:PRO569 4.5 19.9 1.0
SG A:CYS568 4.5 24.7 1.0
N A:ARG516 4.6 27.2 1.0
CB A:LYS517 4.6 19.6 1.0
O A:CYS515 4.6 28.4 1.0
SG A:CYS518 4.6 23.4 1.0
CE1 A:PHE511 4.8 22.7 1.0
SG A:CYS512 4.8 22.6 1.0
N A:CYS518 4.8 24.8 1.0
CD1 A:PHE511 5.0 22.2 1.0

Iron binding site 3 out of 24 in 6zy0

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Iron binding site 3 out of 24 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:23.6
occ:1.00
FE3 A:SF4701 0.0 23.6 1.0
SG A:CYS568 2.3 24.7 1.0
S2 A:SF4701 2.3 20.4 1.0
S1 A:SF4701 2.3 24.4 1.0
S4 A:SF4701 2.3 28.6 1.0
FE1 A:SF4701 2.7 25.8 1.0
FE4 A:SF4701 2.7 23.8 1.0
FE2 A:SF4701 2.7 23.8 1.0
CB A:CYS568 3.1 27.2 1.0
CA A:CYS568 3.8 27.4 1.0
S3 A:SF4701 3.9 27.6 1.0
CD1 A:LEU479 3.9 20.7 1.0
CD A:PRO569 3.9 23.2 1.0
CD1 A:TRP570 4.4 20.6 1.0
N A:PRO569 4.5 24.8 1.0
C A:CYS568 4.6 26.9 1.0
SG A:CYS518 4.6 23.4 1.0
SG A:CYS515 4.8 21.4 1.0
SG A:CYS512 4.8 22.6 1.0
CB A:CYS518 4.9 24.4 1.0
CD1 A:ILE474 4.9 18.1 1.0
N A:CYS568 4.9 31.7 1.0

Iron binding site 4 out of 24 in 6zy0

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Iron binding site 4 out of 24 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:23.8
occ:1.00
FE4 A:SF4701 0.0 23.8 1.0
S2 A:SF4701 2.3 20.4 1.0
S1 A:SF4701 2.3 24.4 1.0
SG A:CYS512 2.3 22.6 1.0
S3 A:SF4701 2.3 27.6 1.0
FE3 A:SF4701 2.7 23.6 1.0
FE1 A:SF4701 2.7 25.8 1.0
FE2 A:SF4701 2.7 23.8 1.0
CB A:CYS512 3.6 25.9 1.0
S4 A:SF4701 3.9 28.6 1.0
CA A:CYS512 3.9 23.7 1.0
CB A:ARG473 4.2 19.8 1.0
N A:ARG473 4.2 20.0 1.0
CB A:CYS515 4.5 19.9 1.0
CD1 A:LEU479 4.6 20.7 1.0
N A:CYS512 4.7 24.0 1.0
SG A:CYS568 4.7 24.7 1.0
SG A:CYS515 4.7 21.4 1.0
CB A:SER472 4.8 17.2 1.0
CA A:ARG473 4.8 15.8 1.0
SG A:CYS518 4.9 23.4 1.0
CD1 A:LEU508 4.9 18.6 1.0
CD1 A:PHE511 4.9 22.2 1.0

Iron binding site 5 out of 24 in 6zy0

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Iron binding site 5 out of 24 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:24.4
occ:1.00
FE1 A:SF4702 0.0 24.4 1.0
S2 A:SF4702 2.3 26.1 1.0
SG A:CYS548 2.3 24.5 1.0
S3 A:SF4702 2.3 25.8 1.0
S4 A:SF4702 2.3 28.4 1.0
FE4 A:SF4702 2.7 27.2 1.0
FE2 A:SF4702 2.7 25.1 1.0
FE3 A:SF4702 2.7 26.5 1.0
CB A:CYS548 3.4 21.6 1.0
S1 A:SF4702 3.9 29.1 1.0
CA A:CYS548 4.1 20.9 1.0
CD A:ARG552 4.3 21.3 1.0
C42 A:B12703 4.4 19.3 1.0
CG A:ARG552 4.4 22.9 1.0
O A:CYS548 4.6 26.6 1.0
C8 A:B12703 4.7 19.9 1.0
C A:CYS548 4.7 22.8 1.0
SG A:CYS522 4.8 26.9 1.0
SG A:CYS561 4.8 28.3 1.0
SG A:CYS564 4.8 24.1 1.0
C41 A:B12703 4.8 20.2 1.0
N45 A:B12703 4.9 17.0 1.0
CB A:ALA526 5.0 22.7 1.0

Iron binding site 6 out of 24 in 6zy0

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Iron binding site 6 out of 24 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:25.1
occ:1.00
FE2 A:SF4702 0.0 25.1 1.0
S4 A:SF4702 2.3 28.4 1.0
SG A:CYS561 2.3 28.3 1.0
S3 A:SF4702 2.3 25.8 1.0
S1 A:SF4702 2.3 29.1 1.0
FE1 A:SF4702 2.7 24.4 1.0
FE3 A:SF4702 2.7 26.5 1.0
FE4 A:SF4702 2.7 27.2 1.0
CB A:CYS561 3.4 22.9 1.0
S2 A:SF4702 3.9 26.1 1.0
N A:ARG563 4.1 24.6 1.0
C A:CYS561 4.1 27.7 1.0
CD A:PRO523 4.2 26.3 1.0
N A:GLY562 4.3 31.7 1.0
O A:CYS561 4.4 29.5 1.0
CA A:CYS561 4.4 28.3 1.0
CD2 A:TYR551 4.5 23.5 1.0
CB A:ARG563 4.6 24.5 1.0
SG A:CYS564 4.7 24.1 1.0
CA A:GLY562 4.7 22.9 1.0
SG A:CYS548 4.8 24.5 1.0
SG A:CYS522 4.8 26.9 1.0
N A:CYS564 4.8 29.4 1.0
C A:GLY562 4.8 24.4 1.0
CE2 A:TYR551 4.8 28.1 1.0
CG A:ARG552 4.9 22.9 1.0
CG A:PRO523 4.9 25.9 1.0
CA A:ARG563 4.9 26.0 1.0

Iron binding site 7 out of 24 in 6zy0

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Iron binding site 7 out of 24 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:26.5
occ:1.00
FE3 A:SF4702 0.0 26.5 1.0
S4 A:SF4702 2.3 28.4 1.0
S1 A:SF4702 2.3 29.1 1.0
S2 A:SF4702 2.3 26.1 1.0
SG A:CYS564 2.3 24.1 1.0
FE2 A:SF4702 2.7 25.1 1.0
FE1 A:SF4702 2.7 24.4 1.0
FE4 A:SF4702 2.7 27.2 1.0
CB A:CYS564 3.1 23.7 1.0
N A:CYS564 3.8 29.4 1.0
S3 A:SF4702 3.9 25.8 1.0
CA A:CYS564 4.1 23.5 1.0
C41 A:B12703 4.5 20.2 1.0
CD1 A:ILE527 4.6 17.3 1.0
C42 A:B12703 4.6 19.3 1.0
N A:ARG563 4.7 24.6 1.0
SG A:CYS561 4.7 28.3 1.0
N45 A:B12703 4.7 17.0 1.0
SG A:CYS548 4.8 24.5 1.0
SG A:CYS522 4.8 26.9 1.0
C8 A:B12703 4.8 19.9 1.0
C A:GLY562 4.9 24.4 1.0
C43 A:B12703 5.0 23.3 1.0

Iron binding site 8 out of 24 in 6zy0

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Iron binding site 8 out of 24 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:27.2
occ:1.00
FE4 A:SF4702 0.0 27.2 1.0
S2 A:SF4702 2.3 26.1 1.0
S1 A:SF4702 2.3 29.1 1.0
SG A:CYS522 2.3 26.9 1.0
S3 A:SF4702 2.3 25.8 1.0
FE1 A:SF4702 2.7 24.4 1.0
FE3 A:SF4702 2.7 26.5 1.0
FE2 A:SF4702 2.7 25.1 1.0
CB A:CYS522 3.4 27.6 1.0
S4 A:SF4702 3.9 28.4 1.0
CA A:CYS522 4.0 26.6 1.0
CD A:PRO523 4.0 26.3 1.0
SG A:CYS524 4.3 30.8 1.0
CB A:ALA526 4.4 22.7 1.0
N A:PRO523 4.4 28.0 1.0
C A:CYS522 4.5 28.9 1.0
SG A:CYS548 4.7 24.5 1.0
SG A:CYS561 4.8 28.3 1.0
SG A:CYS564 4.8 24.1 1.0
CD1 A:ILE527 4.9 17.3 1.0
CB A:CYS564 4.9 23.7 1.0
CG1 A:ILE527 5.0 21.2 1.0
N A:ALA526 5.0 23.5 1.0

Iron binding site 9 out of 24 in 6zy0

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Iron binding site 9 out of 24 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:29.6
occ:1.00
FE1 B:SF4701 0.0 29.6 1.0
S4 B:SF4701 2.3 30.1 1.0
SG B:CYS518 2.3 27.1 1.0
S3 B:SF4701 2.3 31.4 1.0
S2 B:SF4701 2.3 27.0 1.0
FE2 B:SF4701 2.7 31.8 1.0
FE4 B:SF4701 2.7 29.9 1.0
FE3 B:SF4701 2.7 30.1 1.0
CB B:CYS518 3.4 30.1 1.0
S1 B:SF4701 3.9 22.0 1.0
CB B:ARG473 3.9 23.7 1.0
N B:CYS518 4.0 36.7 1.0
CA B:CYS518 4.3 30.9 1.0
CD B:ARG473 4.4 26.4 1.0
CG1 B:ILE474 4.4 24.1 1.0
CG B:ARG473 4.5 25.2 1.0
N B:ILE474 4.6 28.8 1.0
SG B:CYS515 4.7 31.3 1.0
SG B:CYS512 4.7 35.8 1.0
N B:LYS517 4.8 31.6 1.0
CA B:ARG473 4.8 23.8 1.0
N B:ARG473 4.8 24.9 1.0
SG B:CYS568 4.9 34.9 1.0
C B:ARG473 4.9 26.7 1.0

Iron binding site 10 out of 24 in 6zy0

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Iron binding site 10 out of 24 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:31.8
occ:1.00
FE2 B:SF4701 0.0 31.8 1.0
S4 B:SF4701 2.3 30.1 1.0
S3 B:SF4701 2.3 31.4 1.0
SG B:CYS515 2.3 31.3 1.0
S1 B:SF4701 2.3 22.0 1.0
FE1 B:SF4701 2.7 29.6 1.0
FE3 B:SF4701 2.7 30.1 1.0
FE4 B:SF4701 2.7 29.9 1.0
CB B:CYS515 3.1 26.1 1.0
CD B:PRO569 3.9 24.5 1.0
S2 B:SF4701 3.9 27.0 1.0
C B:CYS515 4.3 28.7 1.0
N B:LYS517 4.3 31.6 1.0
CA B:CYS515 4.3 29.6 1.0
CG B:PRO569 4.5 23.8 1.0
O B:CYS515 4.6 32.7 1.0
N B:ARG516 4.6 28.8 1.0
CE1 B:PHE511 4.6 28.5 1.0
SG B:CYS568 4.6 34.9 1.0
SG B:CYS518 4.7 27.1 1.0
CB B:LYS517 4.7 28.4 1.0
SG B:CYS512 4.8 35.8 1.0
CD1 B:PHE511 4.8 28.4 1.0
N B:CYS518 4.8 36.7 1.0
CA B:CYS512 5.0 28.9 1.0

Reference:

T.Halliwell, K.Fisher, K.A.P.Payne, S.E.J.Rigby, D.Leys. Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope. Microorganisms V. 8 2020.
ISSN: ISSN 2076-2607
PubMed: 32887524
DOI: 10.3390/MICROORGANISMS8091344
Page generated: Sun Dec 13 18:29:50 2020

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